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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagagtattagcttgaaaatttccaaattattgcagcggtcttcattttttttgtggactgaacatgtacttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAAGTATGCAT

Basic information

species Zea mays
transcript GRMZM2G159369_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159369_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg--gtcttcattttttttgtggact-gaacatgtacttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAAGTATGCAT
||||||||   |      ||  ||| ||| || |||| || ||||  |   | ||  | |||| | |  |||  ||| || ||||   ||||||||||||||||||| ||||| ||||  ||||| || || |||||||| ||||||||| ||||||||||||| ||||||| |||||| || ||        
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA--------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|22819386|gb|BU499476.1|BU499476
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAG
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAG
EST: gi|148935523|gb|EC879564.2|EC879564
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|24763723|gb|CA398894.1|CA398894
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32837026|gb|CD976704.1|CD976704
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|21891538|gb|BQ744751.1|BQ744751
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32858375|gb|CD998056.1|CD998056
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGAC
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGAC
EST: gi|9254368|gb|BE344836.1|BE344836
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|88755206|gb|DY539347.1|DY539347
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTTCAAGCAG
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTT-CAAGCAG
EST: gi|111145784|gb|EE258169.1|EE258169
EST:     GTGTGGTCACTGCAAGCATCTTTGCTCCG                         ATTTATGAGAAAGCTGGCTTCAGTTTTCAAGCAAGACG
genomic: GTGTGGTCACTGCAAGCATCTT-GCTCCGgttagtagag ... ttaaatttagATTTATGAGAA-GCTGGCTTCAGTTTTCAAGCAGGACG
EST: gi|33285626|gb|CF075421.1|CF075421
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCANGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|211334955|gb|FK966344.1|FK966344
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCA-GCAGGACGACGGGTGT-GTGAT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGG-TGTTGTGAT
EST: gi|31360143|gb|CD444500.1|CD444500
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGAC
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGAC
EST: gi|20507142|gb|BQ279504.1|BQ279504
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|26457090|gb|CA828673.1|CA828673
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGC
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGC
EST: gi|6994161|gb|AW453375.1|AW453375
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32864543|gb|CF004225.1|CF004225
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTNTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|22935460|gb|BU571735.1|BU571735
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|211001445|gb|FL439450.1|FL439450
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattattgcagcggtcttcattttttttgtggactgaacatgtacttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAAGTATGCAT
                                       atgtacttaaattta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtagagtattagcttgaaaatttccaaattattgcagcggtcttcattttttttgtggactgaacatgtacttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAAGTATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG